MetroNome genotype/phenotype database visualization tools

1. MetroNomeTM
Visualizer is a web application
that provides access to the New York Genome
Center’s genomic database through an interac-
tive graphical user interface for integrated
analysis of “-omics” data, related clinical
information, and patient-provided data.
MetroNomeTM
was conceived to explore and
organize data along many dimensions: inves-
tigators can analyze differences at specific
points in the genomes, in specific genes, or
multiple regions. MetroNomeTM
visualizer en-
ables investigators to search for genomic dif-
ferences across large populations, investigate
the effects of genomic variations, and relate
them to phenotypic conditions.
We plan to make MetroNomeTM
available to all
medical researchers to explore public data or
their own datasets. Users will be able to dis-
play and save search results in the portal.
Access to the data will, of course, be subject
to strict access control and the appropriate
approval process.
Drop off your business card
to be invited to our beta test!
MetroNome
TM
SAMPLES VARIANTSGENES124 1067323SAMPLES VARIANTS124 1067GENES 323
MetroNome Visualizer Signed in as Lois Lane
Abbreviated query here [see more]Results Edit query
Samples
ID Gender Age Diabetic Stroke Cardiac Smoking BMI Creatinine LDL Chol. HIV Rubella BRCA1 BRCA2 Blood Type RF antibodyHypertension
45
70
59
88
104
98
49
A+
A-
B+
O+
B+
AB+
O-
B-
B-
A+
AB-
Abbreviated query here [see more]Results Edit query
BRAFOverview next 10 » Genome Browser
Results Edit queryAbbreviated query here [see more]
DAB2 HRAS CACNG3 MAP2K2 COX7B MYL4 ACTC1 UQCRB MAP2K5
RBD Pkinase_TyrC1_15'
5'
3'
3'
Impact
High
Moderate
Low
1 200 300100 400 500 600 700 734 aa
43,889,500 43,890,000 43,890,500 43,891,000 nt
0
5
# of Samples
BRAF-001
Domains
BRAF-002
BRAF-003
BRAF-004
5 Alternate transcripts (click to load into view)
Protein-coding
Protein-coding
Nonsense mediated decay
Retained intron
S428T
Choose columns
Chrom Position rsID SnpEff ENCODERegulome
score
C /T 1 55512190 rs512159 High
Moderate
Modifier
splice region 1 121374 00.008239
G/T 1 55512192 rs121622 splice region 1 121376 00.008239
A/C 1 55512194 rs812164 splice
acceptor
1 121372 00.008239
1
1
1
1
1
1
0.008239
0.008239
0.008239
0.008239
0.008239
0.008239
0.008239
0.008239
0.008239
Ref/Alt
Protein
Consequence
Annotation
Allele
Count
Allele
Number
Number of
Homozygotes
Allele
Frequency
Gene
Allele Freq.
1000 Gen.
Allele Freq.
ExAc
Allele Freq.
MetroNome
18468 533
Current Selection
Samples VariantsGenes
Save Download
Visual Data
Exploration
for a Genomic
Data Warehouse
In the ‘Samples’ tab, the query
results are visualized using in-
teractive diagrams that show
the clinical data associated
with each selected sample set.
On the left, a parallel coordi-
nates plot represents each
sample as a line running from
one dimension to the next,
crossing each axis at the point
of the associated value. On the
right, each horizontal axis is
split into the percentages of
associated metadata present in
the set of samples: diabetic
and not diabetic, non-smoker,
etc. The two diagrams and the
table below are linked, so se-
lections made in one place are
reflected in all three.
The ‘Genes’ tab
shows a gene dia-
gram with annotat-
ed domains from
PFAM at the top,
and the transcript
at the bottom.
Exons are mapped
to the domains,
and mutations are
shown as lollipop
plots, with their
height correspond-
ing to the number
of occurrences in
the sample set.
The ‘Variants’ tab
will show frequen-
cies of variants
across the chro-
mosomes and will
allow comparison
with other data-
bases (dbSNP, 1000
Genomes, ExAC).
Also shown is a
co-occurrence
graph to identify
common variants.
Christian Stolte, Steven Dzik, Sergei German,
Kevin Shi, Sudeep Mehrotra,
Dimitrije Jevremovic, Nina Lapchyk,
Julianna Maniscalco, Karen Hackett,
Shailu Gargeya, Toby Bloom
IN DEVELOPMENT: Variant analysis
SAMPLES VARIANTSGENES124 1067323SAMPLES VARIANTS124 1067
MetroNome Visualizer Signed in as Lois Lane
Abbreviated query here [see more]Results Edit queryResults Edit query
Hide Co-occurance
Variants
Distribution:
A: 12
T: 15
AT: 9
G: 8
A T: 8
T AT: 8
A T AT G:3
A
T
AT
G
Samples
0 5 10 15 20 25
Variants common in this query
Abbreviated query here [see more]
Choose columns
Chrom Position rsID SnpEff ENCODERegulome
score
C / T 1 55512190 rs512159 High
Moderate
Modifier
High
splice region 1 121374 00.008239
G / T 1 55512192 rs121622 splice region 1 121376 00.008239
A / C 1 55512194 rs812164 splice
acceptor
1 121372 00.008239
C / A 1 55512197 rs518806 p.Ala134Asp BRAF missense 1 121374 00.008239
1
1
1
1
1
1
1
1
0.008239
0.008239
0.008239
0.008239
0.008239
0.008239
0.008239
0.008239
0.008239
0.008239
0.008239
0.008239
Ref/Alt
Protein
Consequence
Annotation
Allele
Count
Allele
Number
Number of
Homozygotes
Allele
Frequency
Gene
Allele Freq.
1000 Gen.
Allele Freq.
ExAc
Allele Freq.
MetroNome
1 3 10
Variant frequency for selected query
Comparison in not in: dbSNP 1000Genomes ExAC
pathogenicFilter: rare
Select reference DBs
1 3 10
0.0008329 MetroNome Allele Frequency Cut-off
0.00950
Allele Frequency Cut-off
0.00000
Allele Frequency Cut-off
18468 533
Current Selection
Samples VariantsGenes
Save Download
demo_account